Contacts of the helix formed by residues 396 - 411 (chain A) in PDB entry 3H8E
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A GLY 3.5 1.2 - - - -
395A ASN* 1.3 90.1 - - - +
397A ASP* 1.3 70.8 + - - +
398A ASP* 4.0 13.8 + - - +
399A LEU* 3.3 23.5 + - + +
400A VAL* 3.1 25.4 + - - +
459A ASN* 3.3 41.8 - - + +
460A TRP 4.0 1.7 + - - +
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Residues in contact with ASP 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ASN 5.7 0.2 - - - -
396A ASN* 1.3 77.2 + - - +
398A ASP* 1.3 67.5 + - - +
400A VAL* 3.4 5.8 + - - +
401A GLY* 2.9 20.8 + - - -
416A GLN* 4.8 11.1 + - - -
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Residues in contact with ASP 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A ASN* 3.3 14.6 + - - +
397A ASP* 1.3 84.5 - - - +
399A LEU* 1.3 57.8 + - - +
401A GLY* 3.3 2.0 + - - -
402A GLN* 2.9 42.1 + - + +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A ALA* 4.1 13.0 - - + -
371A VAL 4.2 4.3 - - - +
372A ILE* 4.3 2.9 - - + -
396A ASN* 3.3 21.5 + - + +
397A ASP 3.3 0.4 - - - -
398A ASP* 1.3 78.0 - - - +
400A VAL* 1.4 65.3 + - - +
402A GLN* 3.2 11.9 + - - +
403A LEU* 3.0 38.2 + - + +
459A ASN* 3.7 10.8 - - + +
460A TRP* 3.6 40.8 - - - +
461A ALA* 3.7 7.2 - - + +
490A TYR* 3.5 37.0 - - + +
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Residues in contact with VAL 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 3.9 10.1 - - + -
393A MET 4.2 5.2 - - - +
394A GLY* 3.9 32.1 - - - +
396A ASN 3.1 22.3 + - - +
397A ASP* 3.9 6.5 - - - +
399A LEU* 1.4 74.3 - - - +
401A GLY* 1.3 59.0 + - - +
403A LEU* 3.2 4.3 + - - -
404A LEU* 2.2 52.2 + - + +
416A GLN* 3.7 36.1 - - + +
460A TRP 5.0 0.2 - - - +
461A ALA* 4.5 7.6 - - + -
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Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A ASP 2.9 15.7 + - - -
398A ASP* 3.7 3.4 - - - -
399A LEU 3.2 0.2 - - - -
400A VAL* 1.3 78.9 - - - +
402A GLN* 1.3 56.9 + - - +
404A LEU* 3.4 11.0 + - - +
405A ASP* 2.9 30.7 + - - +
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A ASP* 2.9 26.0 + - + +
399A LEU* 3.4 18.6 - - - +
401A GLY* 1.3 76.3 - - - +
403A LEU* 1.3 59.3 + - - +
405A ASP* 3.4 5.4 + - - +
406A ALA* 2.9 29.1 + - - +
409A ARG* 5.1 0.2 + - - -
490A TYR* 3.6 21.6 + - + -
493A ASP* 4.7 2.8 - - - +
494A ARG* 3.6 45.8 + - - +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A ILE* 3.8 21.5 - - + -
392A LEU* 3.9 20.9 - - + -
399A LEU* 3.0 29.5 + - + +
400A VAL* 3.7 5.6 - - - +
402A GLN* 1.3 74.6 - - - +
404A LEU* 1.3 60.3 + - - +
406A ALA* 3.4 4.1 + - - +
407A GLY 2.9 24.3 + - - -
461A ALA* 3.5 32.3 - - + -
463A MET* 4.8 2.5 - - - -
486A LEU* 3.6 33.8 - - + +
487A LEU* 4.8 4.5 - - + -
490A TYR* 3.6 28.3 - - + -
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A LEU* 2.5 35.9 - - + -
400A VAL* 2.2 49.7 + - + +
401A GLY* 3.8 8.1 - - - +
403A LEU* 1.3 75.6 - - - +
405A ASP* 1.3 62.9 + - - +
407A GLY* 3.2 2.9 + - - -
408A LYS* 3.0 37.4 + - - +
414A ALA* 5.0 17.8 + - - +
415A TRP* 5.4 1.8 - - + -
416A GLN* 4.4 22.4 - - + +
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Residues in contact with ASP 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A GLY 2.9 17.1 + - - +
402A GLN* 3.9 5.4 - - - +
404A LEU* 1.3 77.7 - - - +
406A ALA* 1.4 63.6 + - - +
408A LYS* 3.2 19.1 + - - +
409A ARG* 2.7 57.5 + - - +
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Residues in contact with ALA 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402A GLN 2.9 18.3 + - - +
403A LEU* 3.6 4.9 - - - +
405A ASP* 1.4 75.9 - - - +
407A GLY* 1.3 57.9 + - - +
409A ARG* 3.3 5.9 + - - +
410A ALA* 2.9 31.7 + - - +
486A LEU* 3.7 10.1 - - + +
489A GLN* 3.5 14.3 - - + +
490A TYR* 3.6 33.2 - - + +
493A ASP* 3.9 4.9 - - - +
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Residues in contact with GLY 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A LEU 2.9 11.9 + - - -
404A LEU 3.2 3.1 + - - -
406A ALA* 1.3 76.9 - - - +
408A LYS* 1.4 61.7 + - - +
411A ASP* 3.0 4.7 + - - -
412A ASP 2.9 47.7 + - - -
413A ARG* 3.8 7.0 - - - +
414A ALA 4.8 0.4 - - - -
486A LEU* 3.6 16.3 - - - +
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Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 4.7 0.7 - - - +
120A ARG* 3.1 17.3 + - - -
404A LEU* 3.0 30.5 + - - +
405A ASP* 3.6 19.9 + - - +
407A GLY* 1.4 75.1 - - - +
409A ARG* 1.3 64.6 + - + +
411A ASP* 3.2 7.3 + - - -
413A ARG* 4.1 21.9 - - + +
415A TRP* 6.2 4.0 - - - -
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Residues in contact with ARG 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ARG* 2.8 28.5 + - - +
128A ARG* 4.7 3.8 + - - +
129A LEU* 4.3 4.0 - - - +
402A GLN 5.1 0.2 + - - -
405A ASP* 2.7 46.6 + - - +
406A ALA* 3.8 9.2 - - - +
408A LYS* 1.3 79.6 - - + +
410A ALA* 1.4 59.6 + - - +
489A GLN* 3.3 23.1 + - - +
493A ASP* 2.7 44.6 + - - -
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Residues in contact with ALA 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 4.2 5.2 + - - -
128A ARG* 4.0 15.2 + - - +
129A LEU* 4.6 5.2 - - - +
132A GLU* 4.3 7.4 - - - +
406A ALA 2.9 17.6 + - - +
407A GLY 4.1 2.2 - - - +
409A ARG* 1.4 76.7 - - - +
411A ASP* 1.3 69.3 + - - +
412A ASP* 4.2 3.3 - - - +
485A PRO* 3.7 39.7 - - + +
486A LEU* 4.2 2.7 - - - +
489A GLN* 3.9 8.1 - - + -
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Residues in contact with ASP 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.9 14.2 - - - +
87A ARG* 2.8 46.4 + - - -
90A ARG* 2.9 32.8 + - - +
120A ARG* 3.8 14.8 - - - +
129A LEU* 4.1 7.2 - - + -
407A GLY 3.0 6.1 + - - -
408A LYS 3.2 9.5 + - - -
409A ARG 3.3 0.6 - - - -
410A ALA* 1.3 80.5 - - - +
412A ASP* 1.4 58.7 + - - +
413A ARG* 3.9 13.3 + - - +
482A ARG* 5.4 1.9 + - - -
485A PRO* 5.6 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il